BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438270.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 509,406,144 number of mapped reads = 507,764,857 (99.68%) number of supplementary alignments = 8,323,769 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 254,054,646 number of mapped paired reads (second in pair) = 253,710,211 number of mapped paired reads (both in pair) = 506,606,914 number of mapped paired reads (singletons) = 1,157,943 number of mapped bases = 72,954,069,433 bp number of sequenced bases = 72,934,241,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 178,510,011 duplication rate = 32.6% >>>>>>> Insert size mean insert size = 38,873.4082 std insert size = 1,920,199.138 median insert size = 251 >>>>>>> Mapping quality mean mapping quality = 54.9882 >>>>>>> ACTG content number of A's = 22,109,625,885 bp (30.31%) number of C's = 14,526,107,440 bp (19.92%) number of T's = 21,088,875,108 bp (28.91%) number of G's = 15,209,083,709 bp (20.85%) number of N's = 549,456 bp (0%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 372,986,265 number of insertions = 9,023,374 mapped reads with insertion percentage = 1.75% number of deletions = 7,976,483 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 23.5663X std coverageData = 101.7591X There is a 91.3% of reference with a coverageData >= 1X There is a 90.38% of reference with a coverageData >= 2X There is a 89.27% of reference with a coverageData >= 3X There is a 88% of reference with a coverageData >= 4X There is a 86.53% of reference with a coverageData >= 5X There is a 84.88% of reference with a coverageData >= 6X There is a 83.04% of reference with a coverageData >= 7X There is a 81.04% of reference with a coverageData >= 8X There is a 78.88% of reference with a coverageData >= 9X There is a 76.59% of reference with a coverageData >= 10X There is a 74.2% of reference with a coverageData >= 11X There is a 71.7% of reference with a coverageData >= 12X There is a 69.14% of reference with a coverageData >= 13X There is a 66.53% of reference with a coverageData >= 14X There is a 63.89% of reference with a coverageData >= 15X There is a 61.25% of reference with a coverageData >= 16X There is a 58.61% of reference with a coverageData >= 17X There is a 55.99% of reference with a coverageData >= 18X There is a 53.41% of reference with a coverageData >= 19X There is a 50.87% of reference with a coverageData >= 20X There is a 48.39% of reference with a coverageData >= 21X There is a 45.97% of reference with a coverageData >= 22X There is a 43.63% of reference with a coverageData >= 23X There is a 41.36% of reference with a coverageData >= 24X There is a 39.17% of reference with a coverageData >= 25X There is a 37.06% of reference with a coverageData >= 26X There is a 35.04% of reference with a coverageData >= 27X There is a 33.11% of reference with a coverageData >= 28X There is a 31.26% of reference with a coverageData >= 29X There is a 29.5% of reference with a coverageData >= 30X There is a 27.81% of reference with a coverageData >= 31X There is a 26.22% of reference with a coverageData >= 32X There is a 24.7% of reference with a coverageData >= 33X There is a 23.26% of reference with a coverageData >= 34X There is a 21.89% of reference with a coverageData >= 35X There is a 20.6% of reference with a coverageData >= 36X There is a 19.38% of reference with a coverageData >= 37X There is a 18.22% of reference with a coverageData >= 38X There is a 17.13% of reference with a coverageData >= 39X There is a 16.11% of reference with a coverageData >= 40X There is a 15.14% of reference with a coverageData >= 41X There is a 14.22% of reference with a coverageData >= 42X There is a 13.36% of reference with a coverageData >= 43X There is a 12.55% of reference with a coverageData >= 44X There is a 11.78% of reference with a coverageData >= 45X There is a 11.07% of reference with a coverageData >= 46X There is a 10.39% of reference with a coverageData >= 47X There is a 9.76% of reference with a coverageData >= 48X There is a 9.16% of reference with a coverageData >= 49X There is a 8.61% of reference with a coverageData >= 50X There is a 8.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5886074440 23.61508435319004 23.527572365249153 chr2 243199373 6481329216 26.65027107615117 93.51777183841659 chr3 198022430 5320495013 26.868143235087057 230.8350718323387 chr4 191154276 4922879683 25.753437411988628 25.859427343389942 chr5 180915260 4717810939 26.07746266953932 35.520912572151204 chr6 171115067 4379626125 25.59462589580145 22.853443749416165 chr7 159138663 3942112115 24.771554823229852 26.99981412690779 chr8 146364022 3840995832 26.242759521872117 23.55846882676542 chr9 141213431 3148008471 22.292557079786555 25.499153280215417 chr10 135534747 3456266678 25.50096380819599 37.492348594320156 chr11 135006516 3446310693 25.526995252584697 20.39205176337623 chr12 133851895 3386536330 25.30062297586448 20.358942923831705 chr13 115169878 2518128896 21.864474806511474 20.02266031234143 chr14 107349540 2325228784 21.660351632619943 26.34891797481905 chr15 102531392 2106654575 20.546434939652432 22.0165206898176 chr16 90354753 1977308276 21.883832453174875 37.01665430501253 chr17 81195210 1749874715 21.551452542582254 27.424239379904424 chr18 78077248 1990935943 25.49956605796352 19.925943492316776 chr19 59128983 1110456902 18.78024693913643 289.55482332869013 chr20 63025520 1595964715 25.322515625416496 22.547169272938337 chr21 48129895 936989773 19.467937193712974 121.44015113633823 chr22 51304566 774239035 15.09103565947717 19.624429310405766 chrMT 16571 413089750 24928.474443304567 9507.646691666896 chrX 155270560 2158182601 13.899496472480038 40.105803016363154 chrY 59373566 368569933 6.207643532813912 19.134109297786352